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initial implementation of automated unit conversion.

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this includes a tester program and implementation into pair style tersoff
This commit is contained in:
Axel Kohlmeyer
2020-06-22 17:57:05 -04:00
parent f5a31fefdc
commit b29b3d52f6
9 changed files with 308 additions and 13 deletions
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18
src/MANYBODY/pair_tersoff.cpp
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@ -49,6 +49,7 @@ PairTersoff::PairTersoff(LAMMPS *lmp) : Pair(lmp)
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
nelements = 0;
elements = NULL;
@ -400,8 +401,16 @@ void PairTersoff::read_file(char *file)
// open file on proc 0
if (comm->me == 0) {
PotentialFileReader reader(lmp, file, "Tersoff");
char * line;
PotentialFileReader reader(lmp, file, "Tersoff", unit_convert_flag);
char *line;
// transparently convert units for supported conversions
int unit_convert = reader.get_unit_convert();
double conversion_factor = utils::get_conversion_factor(utils::ENERGY,
unit_convert);
printf("unit_conver=%d\n",unit_convert);
printf("conversion_factor=%g\n",conversion_factor);
while((line = reader.next_line(NPARAMS_PER_LINE))) {
try {
@ -453,6 +462,11 @@ void PairTersoff::read_file(char *file)
params[nparams].lam1 = values.next_double();
params[nparams].biga = values.next_double();
params[nparams].powermint = int(params[nparams].powerm);
if (unit_convert) {
params[nparams].biga *= conversion_factor;
params[nparams].bigb *= conversion_factor;
}
} catch (TokenizerException & e) {
error->one(FLERR, e.what());
}

1
src/pair.cpp
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@ -66,6 +66,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
no_virial_fdotr_compute = 0;
writedata = 0;
ghostneigh = 0;
unit_convert_flag = utils::NOCONVERT;
nextra = 0;
pvector = NULL;

1
src/pair.h
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@ -53,6 +53,7 @@ class Pair : protected Pointers {
int respa_enable; // 1 if inner/middle/outer rRESPA routines
int one_coeff; // 1 if allows only one coeff * * call
int manybody_flag; // 1 if a manybody potential
int unit_convert_flag; // value != 0 indicates support for unit conversion.
int no_virial_fdotr_compute; // 1 if does not invoke virial_fdotr_compute()
int writedata; // 1 if writes coeffs to data file
int ghostneigh; // 1 if pair style needs neighbors of ghosts

24
src/potential_file_reader.cpp
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@ -31,11 +31,13 @@ using namespace LAMMPS_NS;
PotentialFileReader::PotentialFileReader(LAMMPS *lmp,
const std::string &filename,
const std::string &potential_name) :
const std::string &potential_name,
const int auto_convert) :
Pointers(lmp),
reader(nullptr),
filename(filename),
filetype(potential_name + " potential")
filetype(potential_name + " potential"),
unit_convert(auto_convert)
{
if (comm->me != 0) {
error->one(FLERR, "FileReader should only be called by proc 0!");
@ -155,9 +157,21 @@ TextFileReader * PotentialFileReader::open_potential(const std::string& path) {
utils::logmesg(lmp, fmt::format("Reading potential file {} with DATE: {}\n", filename, date));
}
if (!units.empty() && (units != unit_style)) {
lmp->error->one(FLERR, fmt::format("Potential file {} requires {} units "
"but {} units are in use",filename, units, unit_style));
if (units.empty()) {
unit_convert == utils::NOCONVERT;
} else {
if (units == unit_style) {
unit_convert = utils::NOCONVERT;
} else {
if ((units == "metal") && (unit_style == "real") && (unit_convert | utils::METAL2REAL)) {
unit_convert = utils::METAL2REAL;
} else if ((units == "real") && (unit_style == "metal") && (unit_convert | utils::REAL2METAL)) {
unit_convert = utils::REAL2METAL;
} else {
lmp->error->one(FLERR, fmt::format("Potential file {} requires {} units "
"but {} units are in use",filename, units, unit_style));
}
}
}
return new TextFileReader(filepath, filetype);

18
src/potential_file_reader.h
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@ -28,22 +28,25 @@ namespace LAMMPS_NS
{
class PotentialFileReader : protected Pointers {
protected:
TextFileReader * reader;
TextFileReader *reader;
std::string filename;
std::string filetype;
int unit_convert;
TextFileReader * open_potential(const std::string& path);
TextFileReader *open_potential(const std::string& path);
public:
PotentialFileReader(class LAMMPS *lmp, const std::string &filename, const std::string &potential_name);
PotentialFileReader(class LAMMPS *lmp, const std::string &filename,
const std::string &potential_name,
const int auto_convert = 0);
virtual ~PotentialFileReader();
void ignore_comments(bool value);
void skip_line();
char * next_line(int nparams = 0);
void next_dvector(double * list, int n);
ValueTokenizer next_values(int nparams, const std::string & separators = TOKENIZER_DEFAULT_SEPARATORS);
char *next_line(int nparams = 0);
void next_dvector(double *list, int n);
ValueTokenizer next_values(int nparams, const std::string &separators = TOKENIZER_DEFAULT_SEPARATORS);
// convenience functions
double next_double();
@ -51,6 +54,9 @@ namespace LAMMPS_NS
tagint next_tagint();
bigint next_bigint();
std::string next_string();
// unit conversion info
int get_unit_convert() const { return unit_convert; }
};
} // namespace LAMMPS_NS

30
src/utils.cpp
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@ -583,6 +583,36 @@ std::string utils::get_potential_units(const std::string & path, const std::stri
return "";
}
/* ----------------------------------------------------------------------
return bitmask of supported conversions for a given property
------------------------------------------------------------------------- */
int utils::get_supported_conversions(const int property)
{
if (property == ENERGY) {
return METAL2REAL | REAL2METAL;
}
return NOCONVERT;
}
/* ----------------------------------------------------------------------
return conversion factor for a given property and conversion setting
return 0.0 if unknown.
------------------------------------------------------------------------- */
double utils::get_conversion_factor(const int property, const int conversion)
{
if (property == ENERGY) {
if (conversion == NOCONVERT) {
return 1.0;
} else if (conversion == METAL2REAL) {
return 23.060549;
} else if (conversion == REAL2METAL) {
return 0.04336410204284381954;
}
}
return 0.0;
}
/* ------------------------------------------------------------------ */
extern "C" {

18
src/utils.h
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@ -240,6 +240,24 @@ namespace LAMMPS_NS {
* \return UNITS field if present
*/
std::string get_potential_units(const std::string & path, const std::string & potential_name);
enum { NOCONVERT = 0, METAL2REAL = 1, REAL2METAL = 1<<1 };
enum { UNKNOWN = 0, ENERGY };
/**
* \brief Return bitmask of available conversion factors for a given propert
* \param property property to be converted
* \return bitmask indicating available conversions
*/
int get_supported_conversions(const int property);
/**
* \brief Return unit conversion factor for given property and selected from/to units
* \param property property to be converted
* \param conversion constant indicating the conversion
* \return conversion factor
*/
double get_conversion_factor(const int property, const int conversion);
}
}

5
unittest/formats/CMakeLists.txt
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@ -3,6 +3,11 @@ add_executable(test_atom_styles test_atom_styles.cpp)
target_link_libraries(test_atom_styles PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME AtomStyles COMMAND test_atom_styles WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_executable(test_pair_unit_convert test_pair_unit_convert.cpp)
target_link_libraries(test_pair_unit_convert PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME PairUnitConvert COMMAND test_pair_unit_convert WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
set_tests_properties(PairUnitConvert PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
add_executable(test_potential_file_reader test_potential_file_reader.cpp)
target_link_libraries(test_potential_file_reader PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME PotentialFileReader COMMAND test_potential_file_reader WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})

206
unittest/formats/test_pair_unit_convert.cpp Normal file
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@ -0,0 +1,206 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "atom.h"
#include "force.h"
#include "info.h"
#include "input.h"
#include "lammps.h"
#include "pair.h"
#include "utils.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <cstdio>
#include <cstring>
#include <mpi.h>
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
namespace LAMMPS_NS {
using ::testing::Eq;
// eV to kcal/mol conversion constant (CODATA 2018)
const double ev_convert = utils::get_conversion_factor(utils::ENERGY, utils::METAL2REAL);
const double rel_error = 1.0e-13;
class PairUnitConvertTest : public ::testing::Test {
protected:
LAMMPS *lmp;
Info *info;
double fold[4][3];
void SetUp() override
{
const char *args[] = {"PairUnitConvertTest", "-log", "none", "-echo", "screen", "-nocite"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
if (!verbose) ::testing::internal::CaptureStdout();
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_NE(lmp, nullptr);
if (!verbose) ::testing::internal::CaptureStdout();
info = new Info(lmp);
lmp->input->one("units metal");
lmp->input->one("dimension 3");
lmp->input->one("region box block -4 4 -4 4 -4 4");
lmp->input->one("create_box 2 box");
lmp->input->one("create_atoms 1 single -1.1 1.2 0.0 units box");
lmp->input->one("create_atoms 1 single -1.2 -1.1 0.0 units box");
lmp->input->one("create_atoms 2 single 0.9 1.0 0.0 units box");
lmp->input->one("create_atoms 2 single 1.0 -0.9 0.0 units box");
lmp->input->one("pair_style zero 4.0");
lmp->input->one("pair_coeff * *");
lmp->input->one("mass * 1.0");
lmp->input->one("write_data test_pair_unit_convert.data nocoeff");
lmp->input->one("clear");
if (!verbose) ::testing::internal::GetCapturedStdout();
}
void TearDown() override
{
if (!verbose) ::testing::internal::CaptureStdout();
delete info;
delete lmp;
if (!verbose) ::testing::internal::GetCapturedStdout();
remove("test_pair_unit_convert.data");
}
};
TEST_F(PairUnitConvertTest, zero)
{
// check if the prerequisite pair style is available
if (!info->has_style("pair", "zero")) GTEST_SKIP();
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("units metal");
lmp->input->one("read_data test_pair_unit_convert.data");
lmp->input->one("pair_style zero 6.0");
lmp->input->one("pair_coeff * *");
lmp->input->one("run 0 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
// copy energy and force from first step
double eold = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
double **f = lmp->atom->f;
for (int i = 0; i < 4; ++i)
for (int j = 0; j < 3; ++j)
fold[i][j] = f[i][j];
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("clear");
lmp->input->one("units real");
lmp->input->one("read_data test_pair_unit_convert.data");
lmp->input->one("pair_style zero 6.0");
lmp->input->one("pair_coeff * *");
lmp->input->one("run 0 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
double enew = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
EXPECT_NEAR(ev_convert * eold, enew, fabs(enew * rel_error));
f = lmp->atom->f;
for (int i = 0; i < 4; ++i)
for (int j = 0; j < 3; ++j)
EXPECT_NEAR(ev_convert * fold[i][j], f[i][j], fabs(f[i][j] * rel_error));
}
TEST_F(PairUnitConvertTest, lj_cut)
{
// check if the prerequisite pair style is available
if (!info->has_style("pair", "lj/cut")) GTEST_SKIP();
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("units metal");
lmp->input->one("read_data test_pair_unit_convert.data");
lmp->input->one("pair_style lj/cut 6.0");
lmp->input->one("pair_coeff * * 0.01014286346782117 3.504");
lmp->input->one("run 0 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
// copy energy and force from first step
double eold = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
double **f = lmp->atom->f;
for (int i = 0; i < 4; ++i)
for (int j = 0; j < 3; ++j)
fold[i][j] = f[i][j];
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("clear");
lmp->input->one("units real");
lmp->input->one("read_data test_pair_unit_convert.data");
lmp->input->one("pair_style lj/cut 6.0");
lmp->input->one("pair_coeff * * 0.2339 3.504");
lmp->input->one("run 0 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
double enew = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
EXPECT_NEAR(ev_convert * eold, enew, fabs(enew * rel_error));
f = lmp->atom->f;
for (int i = 0; i < 4; ++i)
for (int j = 0; j < 3; ++j)
EXPECT_NEAR(ev_convert * fold[i][j], f[i][j], fabs(f[i][j] * rel_error));
}
TEST_F(PairUnitConvertTest, tersoff)
{
// check if the prerequisite pair style is available
if (!info->has_style("pair", "tersoff")) GTEST_SKIP();
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("units metal");
lmp->input->one("read_data test_pair_unit_convert.data");
lmp->input->one("pair_style tersoff");
lmp->input->one("pair_coeff * * SiC.tersoff Si C");
lmp->input->one("run 0 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
// copy energy and force from first step
double eold = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
double **f = lmp->atom->f;
for (int i = 0; i < 4; ++i)
for (int j = 0; j < 3; ++j)
fold[i][j] = f[i][j];
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("clear");
lmp->input->one("units real");
lmp->input->one("read_data test_pair_unit_convert.data");
lmp->input->one("pair_style tersoff");
lmp->input->one("pair_coeff * * SiC.tersoff Si C");
lmp->input->one("run 0 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
double enew = lmp->force->pair->eng_vdwl + lmp->force->pair->eng_coul;
EXPECT_NEAR(ev_convert * eold, enew, fabs(enew * rel_error));
f = lmp->atom->f;
for (int i = 0; i < 4; ++i)
for (int j = 0; j < 3; ++j)
EXPECT_NEAR(ev_convert * fold[i][j], f[i][j], fabs(f[i][j] * rel_error));
}
} // namespace LAMMPS_NS
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
int rv = RUN_ALL_TESTS();
MPI_Finalize();
return rv;
}